Hi David, I'd like to add that although the "Chimera selection" region will always keep track of the current Chimera selection, you can copy the region to another name to preserve it (click Copy on the Region Browser). We've been using the word "region" to mean boxed areas on the sequence alignment, and a single region can actually include more than one disjoint box. Here is an example of why you'd want to copy the region: if you wanted to keep a region with all residues near a ligand, you could first select those residues and then Copy the "Chimera selection" region to another name, say, "binding site." Then even when you change the current Chimera selection, the "binding site" region will stay the same. You will want to make the border and interior colors of the copy or copies different from one another, however, so it will not be visually confusing. You can also toggle between showing and not showing a region in the alignment with the "Shown" checkboxes in the Region Browser. Best, Elaine On Dec 1, 2005, at 9:48 AM, David G. Morgan wrote:

Hi,

I'm learning to use the sequence alignment tools in chimera. I know that I can highlight sequences in the alignment window and select residues in the structure, but is it possible to do the opposite? In other words, I'd like to box or otherwise select some residue(s) in the structure and have that region highlighted or otherwise marked in the aligned sequence window.

David Gene Morgan Advanced Microscopy & Proteomics Molecular & Cellular Biology University of California at Davis 530 752 2693 (lab) 530 752 3085 (FAX)

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----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html